Retinoic acid (RA) plays a major role in a variety of developmental processes see Strickland, S. et al., Cell 15, 393-403 (1978); Hogan B. L. M. et al., Nature 291, 235-237 (1981); Roberts, A. B. et al., Academic Press 2, 209-286 (1984); Maden, M., Trends in Genetics 1, 103-107 (1985); Brockes, J. P., Neuron 2, 1285-1294 (1989); Eichele, G., Trends in Genetics 5, 246-251 (1989); and Brockes, J., Nature 345, 766-768 (1990) for references and reviews!. In culture, certain murine and human teratocarcinoma cell lines respond to RA by undergoing differentiation forming, for example, cells which resemble primitive endoderm cells or neurons Strickland, S. et al., Cell 15, 393-403 (1978); Hogan, B. L. M. et al., Nature 291, 235-237 (1981); Andrews, P. W., Developmental Biology 103, 285-293 (1984); Sharma, S. et al., Developmental Biology 125, 246-254 (1988)!. Often, these events are accompanied by specific changes in gene expression (for example, see Wang, S. -Y. et al., Proc. Natl. Acad. Sci. USA 80, 5880-5884 (1983); Marotti, K. R. et al., Developmental Biology 108, 26-31 (1985); LaRosa, G. J. et al., Mol. Cell Biol. 8, 3906-3917 (1988); and Vasios, G. W. et al., Proc. Natl. Acad. Sci. USA 86, 9099-9103 (1989) and references therein). RA has been strongly implicated as an active morphogen in pattern formation, chiefly using the developing chick limb bud and the regenerating urodele amphibian limb blastema as models Maden, M., Trends in Genetics 1, 103-107 (1985); Brockes, J. P., Neuron 2, 1285-1294 (1989); Eichele, G., Trends in Genetics 5, 246-251 (1989); Brockes, J., Nature 345, 766-768 (1990); Thaller, C. et al., Nature 327, 625-628 (1987); and Slack., J. M. W., Nature 327, 553-554 (1987) and references therein!.
The role of RA in controlling such diverse processes has been strengthened by the identification of three related nuclear receptors for RA, termed retinoic acid receptors (RARs) .alpha., .beta. and .gamma., that are members of the steroid/thyroid hormone receptor superfamily of inducible transcriptional enhancer factors (Evans, R. M., Science 240, 889-895 (1988); Green, S. et al., Trends in Genetics 4, 309-314 (1988); Beato, M., Cell 56, 335-344 (1989)!, and which bind RA selectively and with high affinity Petkovich, M. et al., Nature 330, 444-450 (1987); Giguere, V. et al., Nature 330, 624-629 (1987); Brand, N. et al., Nature 332, 850-854 (1988); Benbrook, D. et al., Nature 333, 669-672 (1988); Krust, A. et al., Proc. Natl. Acad. Sci. USA 86, 5310-5314 (1989); Zelent, A. et al., Nature 339, 714-717 (1989)!. The three RAR genes are expressed with varying degrees of tissue specificity during embryonic development and in adult tissues, and are found in a number of cultured cell lines Krust, A. et al., Proc. Natl. Acad. Sci. USA 86, 5310-5314 (1989); Zelent, A. et al., Nature 339, 714-717 (1989); Dolle, P. et al., Nature 342, 702-705 (1989); Kastner, P. et al., Proc. Natl. Acad. Sci. USA 87, 2700-2704 (1990); Ruberte, E. et al., Development 108, 213-222 (1990)!. Alignment of RAR amino acid sequences and their comparison with other nuclear receptors has allowed the definition of six regions within the protein, termed A-F Krust, A. et al., Proc. Natl. Acad. Sci. USA 86, 5310-5314 (1989); Zelent, A. et al., Nature 339, 714-717 (1989); Krust, A. et al., EMBO J. 5, 891-897 (1986)!, including the two highly conserved regions C and E; corresponding to the DNA binding and the ligand binding domains, respectively. In additon, recent evidence indicates that isoforms of mouse and human RAR-.gamma., which differ in the amino-terminal region A and 5' untranslated region (5'-UTR), are generated through alternative splicing Krust, A. et al., Proc. Natl. Acad. Sci. USA 86, 5310-5314 (1989); Kastner, P. et al., Proc. Natl. Acad. Sci. USA 87, 2700-2704 (1990); Giguere V. et al., Mol. Cell. Biol. 10, 2335-2340 (1990)!.
Previously, two partial hRAR-.alpha. complementary DNA (cDNA) sequences, which differed in the 5' region, were published by Petkovich, M. et al., Nature 330, 444-450 (1987) and Giguere, V. et al., Nature 330, 624-629 (1987). The hRAR-.alpha. cDNA clone of Petkovich et al. was deduced to encode a protein of 432 amino acids, though an upstream in-frame termination codon was not seen Petkovich, M. et al., Nature 330, 444-450 (1987)!. In contrast, the clone of Giguere, V. et al., Nature 330, 624-629 (1987) encoded a 462 amino acid protein that began at a methionine codon beyond the 5' border of the Petkovich et al. cDNA clone and was preceded by an in-frame TGA termination codon. Neither of the two cDNA clones was full-length in their 5' region. Described here is the isolation and characterization of cDNA and genomic DNA clones containing the sequences encoding the A region and the whole 5'-untranslated region (5'-UTR) of hRAR-.alpha.. This has led to the determination of the exon-intron organization of the 5' region of hRAR-.alpha. gene and to the isolation of a functional promoter which resembles some RNA polymerase B (II) promoters that lack a TATA box Smale, S. T. et al., Cell 57, 103-113 (1989); Smale, S. T. et al., Proc. Natl. Acad. Sci. USA 87, 4509-4513 (1990)!.